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Chlorine in PDB 6y9e: Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2)

Protein crystallography data

The structure of Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2), PDB code: 6y9e was solved by R.Chaloupkova, J.Damborsky, M.Marek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.62 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 109.580, 166.620, 100.290, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.8

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2) (pdb code 6y9e). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2), PDB code: 6y9e:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 6y9e

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Chlorine binding site 1 out of 12 in the Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:16.2
occ:1.00
 O A:HOH565 3.0 26.2 1.0
NE1 A:TRP104 3.2 15.2 1.0
N A:PRO205 3.4 17.0 1.0
ND2 A:ASN38 3.5 14.4 1.0
CA A:PRO205 3.6 15.4 1.0
CZ A:PHE167 3.6 17.1 1.0
CD A:PRO205 3.7 11.5 1.0
C A:PHE204 3.7 18.8 1.0
CD1 A:TRP104 3.7 14.0 1.0
CB A:PHE204 3.8 13.7 1.0
CE2 A:PHE167 3.8 12.7 1.0
O A:PHE204 3.9 15.7 1.0
CB A:PRO205 3.9 17.2 1.0
CD1 A:LEU208 4.0 16.3 1.0
CE2 A:PHE148 4.1 17.8 1.0
CB A:ASN38 4.1 14.6 1.0
CG A:LEU208 4.2 20.4 1.0
CG A:ASN38 4.3 16.0 1.0
CD2 A:LEU208 4.3 18.5 1.0
CA A:PHE204 4.4 15.5 1.0
CG A:PRO205 4.4 15.9 1.0
CE2 A:TRP104 4.4 17.7 1.0
CE1 A:PHE167 4.7 18.9 1.0
CG A:PHE204 4.8 14.9 1.0
O A:HOH691 4.8 23.4 1.0
CZ A:PHE148 4.9 16.1 1.0
CD2 A:PHE148 5.0 16.8 1.0
C A:PRO205 5.0 16.9 1.0

Chlorine binding site 2 out of 12 in 6y9e

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Chlorine binding site 2 out of 12 in the Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:17.8
occ:1.00
 OG1 A:THR40 3.1 16.9 1.0
NE2 A:GLN102 3.2 17.8 1.0
N A:GLY37 3.3 14.1 1.0
NE2 A:GLN274 3.5 18.6 1.0
CD1 A:ILE44 3.9 19.5 1.0
CA A:HIS36 3.9 14.8 1.0
CD1 A:TYR272 4.0 17.9 1.0
CB A:HIS36 4.0 14.3 1.0
CB A:THR40 4.1 15.9 1.0
C A:HIS36 4.1 12.7 1.0
CG2 A:THR40 4.1 17.3 1.0
CA A:GLY37 4.1 15.5 1.0
CB A:GLN102 4.1 16.9 1.0
CD A:GLN102 4.2 19.4 1.0
CG2 A:ILE44 4.2 18.0 1.0
CE1 A:TYR272 4.2 16.4 1.0
CG A:GLN102 4.3 16.4 1.0
OE1 A:GLN274 4.4 20.7 1.0
CD A:GLN274 4.4 20.0 1.0
C A:GLY37 4.5 17.6 1.0
O A:GLN102 4.5 17.7 1.0
CB A:ASP103 4.6 16.1 1.0
O A:GLY37 4.7 18.2 1.0
CG1 A:ILE44 4.8 19.6 1.0
C A:GLN102 4.8 18.3 1.0
CB A:ILE44 4.9 16.5 1.0

Chlorine binding site 3 out of 12 in 6y9e

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Chlorine binding site 3 out of 12 in the Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:18.8
occ:1.00
 OG1 B:THR40 3.2 16.6 1.0
NE2 B:GLN102 3.2 17.0 1.0
N B:GLY37 3.3 14.6 1.0
NE2 B:GLN274 3.4 20.1 1.0
CA B:HIS36 3.9 13.9 1.0
C B:HIS36 4.1 11.3 1.0
CB B:HIS36 4.1 15.8 1.0
CD1 B:TYR272 4.1 16.8 1.0
CA B:GLY37 4.1 16.0 1.0
CG2 B:ILE44 4.1 18.0 1.0
CD1 B:ILE44 4.2 18.8 1.0
CB B:GLN102 4.2 15.7 1.0
CB B:THR40 4.2 12.6 1.0
CD B:GLN102 4.2 17.7 1.0
CG2 B:THR40 4.2 17.6 1.0
CG B:GLN102 4.3 15.7 1.0
CD B:GLN274 4.3 15.9 1.0
OE1 B:GLN274 4.3 18.5 1.0
CE1 B:TYR272 4.4 16.4 1.0
O B:GLN102 4.5 20.4 1.0
C B:GLY37 4.5 17.4 1.0
CB B:ASP103 4.6 19.6 1.0
O B:GLY37 4.7 17.5 1.0
CG1 B:ILE44 4.8 16.6 1.0
C B:GLN102 4.8 18.2 1.0
CB B:ILE44 4.9 14.7 1.0

Chlorine binding site 4 out of 12 in 6y9e

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Chlorine binding site 4 out of 12 in the Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:16.6
occ:1.00
 NE1 B:TRP104 3.2 16.0 1.0
O B:HOH522 3.2 28.0 1.0
N B:PRO205 3.4 16.9 1.0
ND2 B:ASN38 3.5 15.5 1.0
C B:PHE204 3.6 18.1 0.0
CA B:PRO205 3.6 19.2 1.0
CZ B:PHE167 3.6 15.8 1.0
CD B:PRO205 3.6 15.6 1.0
C B:PHE204 3.7 18.1 1.0
CD1 B:TRP104 3.8 18.2 1.0
CB B:PHE204 3.8 18.2 1.0
CB B:PHE204 3.8 18.1 0.0
O B:PHE204 3.8 18.0 0.0
CE2 B:PHE167 3.9 15.7 1.0
O B:PHE204 3.9 17.9 1.0
CB B:PRO205 4.0 21.4 1.0
CD1 B:LEU208 4.1 22.1 1.0
CB B:ASN38 4.1 16.8 1.0
CE2 B:PHE148 4.2 18.4 1.0
CG B:LEU208 4.2 22.1 1.0
CG B:ASN38 4.3 19.0 1.0
CA B:PHE204 4.3 17.9 0.0
CA B:PHE204 4.4 17.8 1.0
CG B:PRO205 4.4 19.2 1.0
CD2 B:LEU208 4.4 20.2 1.0
CE2 B:TRP104 4.5 15.8 1.0
CE1 B:PHE167 4.7 19.0 1.0
CG B:PHE204 4.7 17.9 0.0
CG B:PHE204 4.7 17.9 1.0
O B:HOH698 4.9 26.3 1.0

Chlorine binding site 5 out of 12 in 6y9e

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Chlorine binding site 5 out of 12 in the Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:20.9
occ:1.00
 O C:HOH538 3.1 26.8 1.0
NE1 C:TRP104 3.2 18.7 1.0
N C:PRO205 3.5 19.0 1.0
ND2 C:ASN38 3.5 19.3 1.0
CA C:PRO205 3.6 22.9 1.0
C C:PHE204 3.7 21.0 1.0
CD C:PRO205 3.7 19.0 1.0
CZ C:PHE167 3.7 22.5 1.0
CB C:PHE204 3.8 19.2 1.0
CD1 C:TRP104 3.8 17.7 1.0
CE2 C:PHE167 3.9 18.1 1.0
CB C:PRO205 4.0 23.2 1.0
CD1 C:LEU208 4.0 18.1 1.0
O C:PHE204 4.0 18.7 1.0
CB C:ASN38 4.1 18.2 1.0
CE2 C:PHE148 4.1 26.9 1.0
CG C:LEU208 4.2 19.9 1.0
CG C:ASN38 4.3 21.0 1.0
CD2 C:LEU208 4.3 18.8 1.0
CG C:PRO205 4.4 22.6 1.0
CA C:PHE204 4.4 19.0 1.0
CE2 C:TRP104 4.5 20.4 1.0
O C:HOH681 4.7 30.4 1.0
CE1 C:PHE167 4.8 25.6 1.0
CG C:PHE204 4.8 18.4 1.0
CZ C:PHE148 4.9 25.9 1.0
OD2 C:ASP103 5.0 22.9 1.0
CD2 C:PHE148 5.0 25.6 1.0

Chlorine binding site 6 out of 12 in 6y9e

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Chlorine binding site 6 out of 12 in the Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:24.1
occ:1.00
 OG1 C:THR40 3.1 21.7 1.0
NE2 C:GLN102 3.2 23.0 1.0
N C:GLY37 3.2 19.1 1.0
NE2 C:GLN274 3.6 23.0 1.0
CA C:HIS36 3.9 18.5 1.0
CD1 C:ILE44 4.0 17.7 1.0
CA C:GLY37 4.0 21.2 1.0
C C:HIS36 4.0 24.7 1.0
CD1 C:TYR272 4.1 21.9 1.0
CB C:HIS36 4.1 19.0 1.0
CB C:GLN102 4.1 20.8 1.0
CB C:THR40 4.1 17.7 1.0
CG2 C:THR40 4.1 20.0 1.0
CD C:GLN102 4.1 25.2 1.0
CG2 C:ILE44 4.2 21.1 1.0
CG C:GLN102 4.3 21.3 1.0
CE1 C:TYR272 4.3 21.9 1.0
OE1 C:GLN274 4.4 22.7 1.0
O C:GLN102 4.4 18.6 1.0
CD C:GLN274 4.4 24.3 1.0
C C:GLY37 4.5 21.3 1.0
CB C:ASP103 4.6 16.5 1.0
O C:GLY37 4.6 20.0 1.0
C C:GLN102 4.7 19.4 1.0
CG1 C:ILE44 4.8 22.4 1.0
CB C:ILE44 4.9 19.8 1.0
CA C:GLN102 5.0 19.0 1.0

Chlorine binding site 7 out of 12 in 6y9e

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Chlorine binding site 7 out of 12 in the Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:23.2
occ:1.00
 O D:HOH535 2.9 27.4 1.0
NE1 D:TRP104 3.3 18.8 1.0
ND2 D:ASN38 3.4 22.5 1.0
N D:PRO205 3.4 18.2 1.0
CZ D:PHE167 3.6 25.6 1.0
CA D:PRO205 3.6 24.0 1.0
C D:PHE204 3.6 21.7 0.6
C D:PHE204 3.7 21.7 0.4
CD D:PRO205 3.7 20.2 1.0
CD1 D:TRP104 3.8 15.6 1.0
CB D:PHE204 3.8 19.8 0.4
CB D:PHE204 3.8 19.8 0.6
CE2 D:PHE167 3.9 27.4 1.0
O D:PHE204 3.9 20.8 0.6
O D:PHE204 3.9 20.8 0.4
CD1 D:LEU208 4.0 22.7 1.0
CB D:PRO205 4.0 25.1 1.0
CB D:ASN38 4.0 21.9 1.0
CG D:LEU208 4.2 21.7 1.0
CE2 D:PHE148 4.2 25.7 1.0
CG D:ASN38 4.2 22.1 1.0
CA D:PHE204 4.3 19.9 0.4
CA D:PHE204 4.4 19.9 0.6
CG D:PRO205 4.4 20.4 1.0
CD2 D:LEU208 4.4 19.3 1.0
CE2 D:TRP104 4.5 21.3 1.0
CE1 D:PHE167 4.7 25.0 1.0
CG D:PHE204 4.7 18.2 0.4
CG D:PHE204 4.8 18.2 0.6
O D:HOH699 4.8 29.7 1.0
OD2 D:ASP103 5.0 20.7 1.0

Chlorine binding site 8 out of 12 in 6y9e

Go back to Chlorine Binding Sites List in 6y9e
Chlorine binding site 8 out of 12 in the Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:22.5
occ:1.00
 OG1 D:THR40 3.1 20.1 1.0
NE2 D:GLN102 3.2 18.1 1.0
N D:GLY37 3.2 20.1 1.0
NE2 D:GLN274 3.4 20.5 1.0
CA D:HIS36 3.8 17.2 1.0
CB D:HIS36 3.9 18.9 1.0
CD1 D:ILE44 4.0 17.4 1.0
C D:HIS36 4.0 21.1 1.0
CD1 D:TYR272 4.1 21.6 1.0
CA D:GLY37 4.1 21.4 1.0
CB D:THR40 4.1 20.9 1.0
CB D:GLN102 4.1 19.3 1.0
CD D:GLN102 4.2 21.0 1.0
CG2 D:THR40 4.2 18.7 1.0
CG2 D:ILE44 4.2 21.3 1.0
CG D:GLN102 4.3 17.1 1.0
CD D:GLN274 4.3 22.1 1.0
CE1 D:TYR272 4.3 22.8 1.0
OE1 D:GLN274 4.3 20.7 1.0
C D:GLY37 4.5 18.8 1.0
O D:GLN102 4.5 17.9 1.0
CB D:ASP103 4.7 20.0 1.0
O D:GLY37 4.7 20.9 1.0
C D:GLN102 4.8 19.0 1.0
CG1 D:ILE44 4.9 19.7 1.0
CB D:ILE44 5.0 22.1 1.0

Chlorine binding site 9 out of 12 in 6y9e

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Chlorine binding site 9 out of 12 in the Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl401

b:24.6
occ:1.00
 O E:HOH521 3.1 33.9 1.0
NE1 E:TRP104 3.2 28.4 1.0
ND2 E:ASN38 3.4 21.1 1.0
N E:PRO205 3.4 23.3 1.0
CZ E:PHE167 3.5 25.8 1.0
CA E:PRO205 3.6 23.0 1.0
C E:PHE204 3.7 23.2 0.1
CD E:PRO205 3.7 21.9 1.0
C E:PHE204 3.7 23.2 0.9
CD1 E:TRP104 3.8 27.9 1.0
CE2 E:PHE167 3.8 22.4 1.0
O E:PHE204 3.9 24.9 0.1
CB E:PHE204 3.9 22.4 0.9
CB E:PHE204 3.9 22.5 0.1
CB E:PRO205 3.9 22.4 1.0
O E:PHE204 4.0 25.0 0.9
CE2 E:PHE148 4.0 27.6 1.0
CD1 E:LEU208 4.1 28.2 1.0
CB E:ASN38 4.1 22.3 1.0
CG E:LEU208 4.2 22.6 1.0
CG E:ASN38 4.2 26.0 1.0
CD2 E:LEU208 4.4 27.3 1.0
CA E:PHE204 4.4 23.2 0.1
CA E:PHE204 4.4 23.2 0.9
CG E:PRO205 4.4 22.3 1.0
CE2 E:TRP104 4.5 24.8 1.0
CE1 E:PHE167 4.6 25.3 1.0
O E:HOH637 4.7 41.5 1.0
CZ E:PHE148 4.8 27.0 1.0
CG E:PHE204 4.8 22.5 0.1
CG E:PHE204 4.8 22.4 0.9
CD2 E:PHE148 4.9 31.2 1.0
C E:PRO205 5.0 24.0 1.0

Chlorine binding site 10 out of 12 in 6y9e

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Chlorine binding site 10 out of 12 in the Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Putative Ancestral Haloalkane Dehalogenase ANCHLD2 (Node 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl402

b:30.5
occ:1.00
 NE2 E:GLN102 3.1 31.4 1.0
OG1 E:THR40 3.2 23.6 1.0
N E:GLY37 3.2 21.8 1.0
NE2 E:GLN274 3.5 30.0 1.0
CA E:HIS36 3.9 22.9 1.0
CD1 E:ILE44 3.9 31.7 1.0
CA E:GLY37 4.0 21.4 1.0
C E:HIS36 4.0 22.4 1.0
CD1 E:TYR272 4.1 31.8 1.0
CB E:HIS36 4.1 21.6 1.0
CG2 E:THR40 4.1 25.0 1.0
CB E:GLN102 4.1 23.8 1.0
CD E:GLN102 4.1 32.4 1.0
CB E:THR40 4.2 23.6 1.0
CG2 E:ILE44 4.2 27.4 1.0
CG E:GLN102 4.3 29.3 1.0
CE1 E:TYR272 4.3 28.3 1.0
CD E:GLN274 4.4 29.9 1.0
O E:GLN102 4.4 27.1 1.0
C E:GLY37 4.4 28.2 1.0
OE1 E:GLN274 4.4 28.6 1.0
CB E:ASP103 4.5 29.1 1.0
O E:GLY37 4.6 26.4 1.0
C E:GLN102 4.7 32.0 1.0
CG1 E:ILE44 4.9 27.9 1.0
CB E:ILE44 5.0 30.0 1.0

Reference:

P.Babkova, Z.Dunajova, R.Chaloupkova, J.Damborsky, D.Bednar, M.Marek. Structures of Hyperstable Ancestral Haloalkane Dehalogenases Show Restricted Conformational Dynamics. Comput Struct Biotechnol J V. 18 1497 2020.
ISSN: ISSN 2001-0370
PubMed: 32637047
DOI: 10.1016/J.CSBJ.2020.06.021
Page generated: Mon Jul 29 17:36:32 2024

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